Re: [R-pkg-devel] How to write example results to a tempdir()?

[Duncan Murdoch]

On 25/04/2018 1:32 PM, Sarah Goslee wrote:

Don't change the working directory! That has all kinds of unpleasant
side effects for the unsuspecting user, possibly even more so than
writing to a file.

Instead, write the file to the temp directory, and read it from there, with e.g.

wd <- tempdir()
write(dat, file.path(wd, 'Ttest_1981-2000.dat'))

Using file.path() means that the appropriate path delimiter for that
OS will be used.


That's one good way to do it.  But it is possible to change directory 
and change back at the end of the example.  For example,


wd <- tempdir()
savedir <- setwd(wd)

... # the original code that writes and reads in the current dir

setwd(savedir)

There's a worry that an error in the middle of the code will leave the 
user in the wrong place.  If that's really unlikely to happen, then this 
code is a little simpler than Sarah's suggestion.


If it is likely, you can use tryCatch(..., finally = setwd(savedir)), 
but I think Sarah's solution would be preferable in most cases:  many 
users will not understand what tryCatch() does.


Duncan Murdoch



Sarah


On Wed, Apr 25, 2018 at 12:30 PM, Jose A Guijarro  wrote:

Dear all,

I am struggling to update my package climatol from version 3.0 to 3.1.
The old version had all examples under a "dontrun" section because they
needed files created by other examples that the user had to run first.

As this is not acceptable anymore, I made the examples runnable and
prepared small ad-hoc datasets, but then writing files to the user space
is against the CRAN policy rules, and I was suggested to run them on a
temporal directory. Therefore I changed all my examples to read/write
files to a tempdir(), as in:

\examples{
#Set a temporal working directory and write input files:
wd <- tempdir()
setwd(wd)
data(Ttest) #(This loads matrix 'dat' and data.frame 'est.c')
write(dat,'Ttest_1981-2000.dat')
write.table(est.c,'Ttest_1981-2000.est',row.names=FALSE,col.names=FALSE)
rm(dat,est.c) #remove loaded data from memory space
#Now run the example:
dd2m('Ttest',1981,2000)
#Input and output files can be found in directory:
print(wd)
}

But now CRAN checks return this warning ten times (one for every example
in the package):

Warning: working directory was changed to ‘/tmp/RtmpWSRK2F’, resetting

Any hint on how to solve the problem will be highly appreciated...

Jose






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Re: [R-pkg-devel] How to write example results to a tempdir()?

[Uwe Ligges]

On 25.04.2018 19:45, Jose A Guijarro wrote:

Many thanks for your advise, Sarah!

I will try to implement it. (Now I will have to change all my reading and
writing sentences of all my functions, because they read/write from/to
the users working directory...)


Whcih is OK if the user specifies some filename.

Best,
Uwe Ligges




Best regards,

     Jose

El 25/04/18 a las 19:32, Sarah Goslee escribió:

Don't change the working directory! That has all kinds of unpleasant
side effects for the unsuspecting user, possibly even more so than
writing to a file.

Instead, write the file to the temp directory, and read it from there, 
with e.g.


wd <- tempdir()
write(dat, file.path(wd, 'Ttest_1981-2000.dat'))

Using file.path() means that the appropriate path delimiter for that
OS will be used.

Sarah


On Wed, Apr 25, 2018 at 12:30 PM, Jose A Guijarro 
 wrote:

Dear all,

I am struggling to update my package climatol from version 3.0 to 3.1.
The old version had all examples under a "dontrun" section because they
needed files created by other examples that the user had to run first.

As this is not acceptable anymore, I made the examples runnable and
prepared small ad-hoc datasets, but then writing files to the user space
is against the CRAN policy rules, and I was suggested to run them on a
temporal directory. Therefore I changed all my examples to read/write
files to a tempdir(), as in:

\examples{
#Set a temporal working directory and write input files:
wd <- tempdir()
setwd(wd)
data(Ttest) #(This loads matrix 'dat' and data.frame 'est.c')
write(dat,'Ttest_1981-2000.dat')
write.table(est.c,'Ttest_1981-2000.est',row.names=FALSE,col.names=FALSE)
rm(dat,est.c) #remove loaded data from memory space
#Now run the example:
dd2m('Ttest',1981,2000)
#Input and output files can be found in directory:
print(wd)
}

But now CRAN checks return this warning ten times (one for every example
in the package):

Warning: working directory was changed to ‘/tmp/RtmpWSRK2F’, resetting

Any hint on how to solve the problem will be highly appreciated...

Jose







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Re: [R-pkg-devel] How to write example results to a tempdir()?

[Jose A Guijarro]

Many thanks for your advise, Sarah!

I will try to implement it. (Now I will have to change all my reading and
writing sentences of all my functions, because they read/write from/to
the users working directory...)

Best regards,

    Jose

El 25/04/18 a las 19:32, Sarah Goslee escribió:

Don't change the working directory! That has all kinds of unpleasant
side effects for the unsuspecting user, possibly even more so than
writing to a file.

Instead, write the file to the temp directory, and read it from there, with e.g.

wd <- tempdir()
write(dat, file.path(wd, 'Ttest_1981-2000.dat'))

Using file.path() means that the appropriate path delimiter for that
OS will be used.

Sarah


On Wed, Apr 25, 2018 at 12:30 PM, Jose A Guijarro  wrote:

Dear all,

I am struggling to update my package climatol from version 3.0 to 3.1.
The old version had all examples under a "dontrun" section because they
needed files created by other examples that the user had to run first.

As this is not acceptable anymore, I made the examples runnable and
prepared small ad-hoc datasets, but then writing files to the user space
is against the CRAN policy rules, and I was suggested to run them on a
temporal directory. Therefore I changed all my examples to read/write
files to a tempdir(), as in:

\examples{
#Set a temporal working directory and write input files:
wd <- tempdir()
setwd(wd)
data(Ttest) #(This loads matrix 'dat' and data.frame 'est.c')
write(dat,'Ttest_1981-2000.dat')
write.table(est.c,'Ttest_1981-2000.est',row.names=FALSE,col.names=FALSE)
rm(dat,est.c) #remove loaded data from memory space
#Now run the example:
dd2m('Ttest',1981,2000)
#Input and output files can be found in directory:
print(wd)
}

But now CRAN checks return this warning ten times (one for every example
in the package):

Warning: working directory was changed to ‘/tmp/RtmpWSRK2F’, resetting

Any hint on how to solve the problem will be highly appreciated...

Jose





--
Firma
Dr. José A. Guijarro
Logotipo de Aemet
Delegación Territorial en Illes Balears
Jefe de la Unidad de Estudios Meteorológicos del Mediterráneo
Tel. (+34) 971145409   (Tno. interno: 50790)
www.aemet.es 
 
 
 



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Re: [R-pkg-devel] How to write example results to a tempdir()?

[Sarah Goslee]

Don't change the working directory! That has all kinds of unpleasant
side effects for the unsuspecting user, possibly even more so than
writing to a file.

Instead, write the file to the temp directory, and read it from there, with e.g.

wd <- tempdir()
write(dat, file.path(wd, 'Ttest_1981-2000.dat'))

Using file.path() means that the appropriate path delimiter for that
OS will be used.

Sarah


On Wed, Apr 25, 2018 at 12:30 PM, Jose A Guijarro  wrote:
> Dear all,
>
> I am struggling to update my package climatol from version 3.0 to 3.1.
> The old version had all examples under a "dontrun" section because they
> needed files created by other examples that the user had to run first.
>
> As this is not acceptable anymore, I made the examples runnable and
> prepared small ad-hoc datasets, but then writing files to the user space
> is against the CRAN policy rules, and I was suggested to run them on a
> temporal directory. Therefore I changed all my examples to read/write
> files to a tempdir(), as in:
>
> \examples{
> #Set a temporal working directory and write input files:
> wd <- tempdir()
> setwd(wd)
> data(Ttest) #(This loads matrix 'dat' and data.frame 'est.c')
> write(dat,'Ttest_1981-2000.dat')
> write.table(est.c,'Ttest_1981-2000.est',row.names=FALSE,col.names=FALSE)
> rm(dat,est.c) #remove loaded data from memory space
> #Now run the example:
> dd2m('Ttest',1981,2000)
> #Input and output files can be found in directory:
> print(wd)
> }
>
> But now CRAN checks return this warning ten times (one for every example
> in the package):
>
> Warning: working directory was changed to ‘/tmp/RtmpWSRK2F’, resetting
>
> Any hint on how to solve the problem will be highly appreciated...
>
> Jose
>


-- 
Sarah Goslee
http://www.functionaldiversity.org

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[R-pkg-devel] How to write example results to a tempdir()?

[Jose A Guijarro]

Dear all,

I am struggling to update my package climatol from version 3.0 to 3.1. 
The old version had all examples under a "dontrun" section because they 
needed files created by other examples that the user had to run first.

As this is not acceptable anymore, I made the examples runnable and 
prepared small ad-hoc datasets, but then writing files to the user space 
is against the CRAN policy rules, and I was suggested to run them on a 
temporal directory. Therefore I changed all my examples to read/write 
files to a tempdir(), as in:

\examples{
#Set a temporal working directory and write input files:
wd <- tempdir()
setwd(wd)
data(Ttest) #(This loads matrix 'dat' and data.frame 'est.c')
write(dat,'Ttest_1981-2000.dat')
write.table(est.c,'Ttest_1981-2000.est',row.names=FALSE,col.names=FALSE)
rm(dat,est.c) #remove loaded data from memory space
#Now run the example:
dd2m('Ttest',1981,2000)
#Input and output files can be found in directory:
print(wd)
}

But now CRAN checks return this warning ten times (one for every example 
in the package):

Warning: working directory was changed to ‘/tmp/RtmpWSRK2F’, resetting

Any hint on how to solve the problem will be highly appreciated...

Jose

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